How do I know the parameter use in Neuron?

[huntadams]

Hello,
I am a beginner to use Neuron. I have some questions about it.

1. I chose "stylized". How do I know the parameters about this program, including sodium channel inactivation time, the diameter of axon, the size of soma, etc.?
How do I change the ion concentration in this program?
Can I export the values of membrane potential change to a text file?

2. The axon is so thin. Based on what I learned, I didn't hear of intracellular recording of axon membrane potential, except giant squid. So, how does Neuron simulate the membrane potential change of axon?

Thanks.

[ted]

How do I know the parameters about this program, including sodium channel inactivation time, the diameter of axon, the size of soma, etc.?

Excellent question, even if there is no such thing as " channel inactivation time."

Be sure to read "Help for the total beginner"
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=177
If you have already read it, read it again--I have revised it to make it more useful to
beginners.

To discover what biological properties are represented in a model, and how they are
represented, you can read the model's source code. If some or all of the biological
properties were specified with GUI tools, examine the settings in those GUI tools.

If the code has already been executed so that a model cell exists, type
topology()
at the oc> prompt in NEURON's xterm (the window where NEURON prints its "welcome"
message when it first starts) to see a teletype-style printout of the branched architecture
of the model. Then type
forall psection()
at the oc> prompt to see the name, length, diameter, and biophysical properties of each
section. Be sure to read about topology(), forall, and psection() in the Programmer's
Reference.

You can also use NEURON's Model View tool
NEURON Main Menu / Tools / Model View
to browse through an outline of model properties.

How do I change the ion concentration in this program?

If a section has a mechanism that uses ionic concentrations, the intra- and extracellular
concentrations for those ions will be known to hoc as nai, nao, ki, ko, etc., and default
initial values for ionic concentrations will be known as nai0_na_ion, nao0_na_ion, etc..
Be sure to read the documentation of ion_style in the Programmer's Reference
http://www.neuron.yale.edu/neuron/stati ... #ion_style
For more information about initiializing ionic concentrations see chapter 8 of
The NEURON Book.

Can I export the values of membrane potential change to a text file?

Record to a Vector. After the simulation, write the Vector to a file. Or, if v is plotted in
a graph, use the graph's Pick vector to copy the voltage trace to NEURON's clipboard,
then use
NEURON Main Menu / Vector / Save to File
to write the voltage and time data to a file. For more information, in this forum see
Saving simulation results
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=51
and
output: numbers instead of graph
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=66

2. The axon is so thin. Based on what I learned, I didn't hear of intracellular recording of axon membrane potential, except giant squid.

Ask for a tuition refund. It has been done. All you need is a grant and some sla--sorry--
graduate students or postdoctoral students who will work endless hours to achieve
amazing results.

So, how does Neuron simulate the membrane potential change of axon?

By numerical solution of the cable equation.